I am pretty sure that thunderbird stores some database’esque files in there, which are changing even if you are not actively using the application. I’ve already explained to you on github how to check what activity has happened which can then explain why the conflicts happened.
I tried syncing thunderbird dbs for backup on another device too at the beginning: It doesn’t work, because it uses multiple db files of which some are locked when thunderbird is running, thus I never got a full, consistent transmission.
See Syncing Email for discussion on sync Thunderbird profile. Works fine if you are careful about closing the application and leaving sufficient time for ST to sync databases across devices. I had several conflicts after the new watcher was enabled but I’ve now disabled watcher on TB folders and set scans to 30 secs, no conflicts since.